New & Noteworthy
New SGD Help Video: Exploring Expression Datasets with SPELL
August 09, 2016
Trying to find relevant expression datasets or genes with similar expression profiles for your favorite genes? Look no further than SPELL – the Serial Pattern of Expression Levels Locator. Given a set of genes, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and pairs the genes in your query with additional coexpressed genes.
To learn the basics of SPELL and find out how to run a query, check out our help video:
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
Categories: Tutorial
Sign Up Now for the Next SGD Webinar: August 3, 2016
July 28, 2016
SGD’s Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used S. cerevisiae strains. Our upcoming webinar on August 3rd, 9:30 AM PDT will provide a quick 10 minute tutorial on how to use Variant Viewer. We will demonstrate how to compare nucleotide and amino acid sequences of different S. cerevisiae genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar4
This is the fourth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Sequence, Tutorial
Next SGD Webinar: June 1, 2016
May 26, 2016
If you’re not already using JBrowse to view all your favorite S. cerevisiae genes…you should be! SGD’s JBrowse is a quick and easy way to browse through the information-rich yeast genome. Using JBrowse, you can visualize spatial relationships between genes, locate SGD annotations throughout the yeast genome, and align chromosomal features to hundreds of experimental data sets.
Our upcoming webinar on June 1st will provide a short 15-minute tutorial on the basics of JBrowse. We will demonstrate how to navigate the genome with JBrowse, locate your favorite genes or chromosomal features, and visualize experimental data with data tracks. Whether you’re an experienced GBrowse user looking to try JBrowse for the first time, or someone new to genome browsing as a whole, this webinar is sure to help you get started.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar3
This is the third episode of the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Tutorial
New SGD Help: Downloading and Uploading JBrowse Data Tracks
May 10, 2016
SGD’s new JBrowse genome browser allows quick and easy browsing of the information-rich yeast genome.
Take a look at our newest video tutorial to learn how to download or upload JBrowse data tracks. Let us know if you have any questions or suggestions.
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
Categories: Tutorial
New SGD Help Video: YeastMine Scenario
March 17, 2016
If you’re not already using YeastMine to answer all your questions about the Saccharomyces cerevisiae genome and the gene products it encodes…you should be! YeastMine enables slicing and dicing of data from SGD in any way you choose. Ask questions like “Which genes can mutate to confer oxidative stress resistance, and what biological processes are they involved in?” or “Are there any undiscovered subunits of the mitochondrial ribosome?”
Take a look at our newest video tutorial to dig into YeastMine, and let us know if you have any questions or suggestions.
For more SGD Help Videos, be sure to visit our YouTube channel!
Categories: Tutorial
New SGD Help Video: Variant Viewer
November 05, 2015
Using SGD’s Variant Viewer, you can compare the nucleotide and protein sequences of your favorite genes in twelve widely-used S. cerevisiae genomes. This tool shows alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome. Sequence data are derived from Song et al., 2015.
Take a look at our new video tutorial to get started with the Variant Viewer, and let us know if you have questions or suggestions.
Categories: Sequence, Tutorial
SGD Help Video: Mutant Phenotypes
November 04, 2015
SGD’s Phenotype pages present detailed information about single mutant phenotypes for a particular gene, along with references for each observation. Phenotype pages are accessible from the ‘Phenotype’ tab of the Locus Summary and is also linked from the Mutant Phenotypes section of the Locus Summary, where the phenotype data are presented in summary form. Data are presented in tabular form on the Phenotype page.
This brief video will give you an overview of the contents and organization of SGD’s Phenotype pages.
Categories: Tutorial
SGD Help Video: Literature Page
October 29, 2015
If you’re interested in finding all the published literature about a gene or protein, there’s no need to wade through long lists of PubMed results. SGD curators have already done that for you! We review PubMed weekly for new papers about S. cerevisiae. You can find papers about a specific gene or protein on its Literature tab page (see an example).
Articles on the Literature page are categorized by several topics. The Primary Literature section lists papers in which the gene of interest is a primary focus of the study, while the Additional Literature section lists papers in which the gene is mentioned but is more peripheral to the research. There are other categories of references, and also a cool interactive graphic that shows the relationships between papers that are about the same set, or overlapping sets, of genes. You can get to the Literature page for a gene or protein via the Literature tab, located at the top of its Locus Summary page and all of its other tab pages.
Categories: Tutorial
Tags: video
New SGD Help Video: GO Term Finder
October 26, 2015
Our GO Term Finder tool lets you start with a list of genes—perhaps a set of genes that are co-regulated, or a group of genes that can all mutate to the same phenotype—and analyze their Gene Ontology (GO) annotations to find out what else they might have in common. GO Term Finder searches for significantly shared terms within the GO annotations associated with the genes in your list. It takes advantage of the tree structure of GO to find terms that are related to each other within the ontology.
Finding shared terms within a gene set can bring meaning to experimental results and suggest new avenues to explore. For example, if the GO Term Finder results show that most of the genes in your co-regulated set mediate steps in a pathway, this might be a hint that the uncharacterized genes in the set also participate in that pathway. Or perhaps GO Term Finder will show that a group of genes that can mutate to confer resistance to a certain drug are all annotated to a certain cellular location, suggesting a mechanism for the effects of that drug. Give it a try and see what interesting results your gene list has in store!
Our new SGD Help video gives you a quick overview of how to use the GO Term Finder. You can find all the details on our GO Term Finder help page.
Categories: Tutorial
Tags: Gene Ontology, GO Term Finder, video
New SGD Help Video: GO Slim Mapper
October 05, 2015
The GO Slim Mapper is a very useful tool that maps specific Gene Ontology (GO) annotations to more general GO terms. This allows you to take a group of genes and bin them into broad categories of function, process, or localization by mapping their GO annotations to broader terms.
Watch our new video to get an overview of how the GO Slim Mapper works:
Categories: Tutorial
Tags: Gene Ontology, GO Slim Mapper, video